Files in dataquieR

Data Quality in Epidemiological Research

NEWS.md README.md R/util_get_vars_in_segment.R R/util_verify_dataquieR_resultset2.R R/summary.dataquieR_resultset.R R/util_parallel_futures.R R/util_generate_pages_from_report.R R/des_scatterplot_matrix.R R/util_get_redcap_rule_env.R R/util_order_of_indicator_metrics.R R/util_get_colors.R R/util_ensure_suggested.R R/prep_check_meta_names.R R/util_par_pmap.R R/util_isolate_function.R R/util_get_code_list.R R/util_readr_cols_from_metadata.R R/util_mime_types.R R/dataquieR-package.R R/util_make_data_slot_from_table_slot.R R/util_prep_location_check.R R/util_app_loess.R R/util_adjust_data_type.R R/as.list.dataquieR_resultset.R R/rbind.R R/acc_loess.R R/con_contradictions_redcap.R R/util_suppress_output.R R/util_verify_names.R R/print.dataquieR_summary.R R/util_normalize_clt.R R/prep_create_meta.R R/util_plot_figure_no_plotly.R R/resnames.dataquieR_resultset2.R R/util_ensure_label.R R/util_set_singlequotes.R R/util_acc_loess_continuous.R R/util_acc_loess_bin.R R/util_optimize_sequence_across_time_var.R R/util_margins_lm.R R/dataquieR_resultset.R R/util_disjunct_var_sets.R R/util_app_hl.R R/util_int_duplicate_ids_dataframe.R R/util_assign_levlabs.R R/util_par_lapply_lb.R R/util_really_rstudio.R R/util_acc_varcomp.R R/util_view_file.R R/prep_combine_report_summaries.R R/int_sts_element_dataframe.R R/util_as_cat.R R/com_segment_missingness.R R/000_globs.R R/util_set_size.R R/util_int_duplicate_ids_segment.R R/util_col_description.R R/prep_remove_from_cache.R R/util_map_by_largest_prefix.R R/prep_render_pie_chart_from_summaryclasses_plotly.R R/statichtmlWidget.R R/util_backtickQuote.R R/util_app_mol.R R/util_tukey.R R/util_check_group_levels.R R/print.dataquieR_resultset2.R R/acc_multivariate_outlier.R R/util_as_valid_missing_codes.R R/util_plotly_font_size.R R/util_parse_interval.R R/util_app_cd.R R/util_html_for_dims.R R/util_storr_factory.R R/util_amend_missing_metadata.R R/util_contradiction_rules.R R/util_alias2caption.R R/util_init_respum_tab.R R/des_summary.R R/util_margins_ord.R R/get_internal_api.R R/util_variable_references.R R/util_sort_by_order.R R/util_get_thresholds.R R/util_get_message_for_result.R R/util_dichotomize.R R/prep_add_computed_variables.R R/util_prep_proportion_check.R R/util_des_functions_env.R R/util_copy_all_deps.R R/util_string_is_not_categorical.R R/util_parallel_classic.R R/print.dataquieR_resultset.R R/des_summary_categorical.R R/util_detect_cores.R R/zzz-dq-lazy-s7.R R/util_translate.R R/com_unit_missingness.R R/util_conversion_stable.R R/util_seg_table.R R/as.data.frame.dataquieR_resultset.R R/util_expect_data_frame.R R/prep_robust_guess_data_type.R R/util_is_na_0_empty_or_false.R R/prep_deparse_assignments.R R/acc_margins.R R/util_all_intro_vars_for_rv.R R/util_plot_svg_to_uri.R R/util_app_sos.R R/util_plot_categorical_vars.R R/util_stop_if_not.R R/prep_add_to_meta.R R/prep_map_labels.R R/util_app_im.R R/util_parse_assignments.R R/prep_extract_summary.dataquieR_result.R R/prep_list_voc.R R/util_int_unexp_records_set_dataframe.R R/util_function_description.R R/meta_data_env.R R/util_create_report_by_overview.R R/util_count_expected_observations.R R/util_merge_data_frame_list.R R/util_dashboard_table.R R/html_dependency_clipboard.R R/prep_prepare_dataframes.R R/util_app_dl.R R/util_replace_hard_limit_violations.R R/prep_min_obs_level.R R/prep_check_for_dataquieR_updates.R R/dq_report_by.R R/util_margins_nom.R R/util_fix_merge_dups.R R/util_message.R R/util_evaluate_calls.R R/prep_list_dataframes.R R/util_validate_known_meta.R R/util_combine_res.R R/prep_get_labels.R R/util_unit2baseunit.R R/prep_merge_study_data.R R/util_setup_rstudio_job.R R/con_limit_deviations.R R/util_observation_expected.R R/prep_apply_coding.R R/util_ensure_character.R R/acc_univariate_outlier.R R/util_app_con_contradictions_redcap.R R/util_avail_ram.R R/util_try_with_trace.R R/util_match_arg.R R/util_get_labels_grading_class.R R/prep_add_missing_codes.R R/util_s3_register.R R/util_expect_scalar.R R/util_plotly_text.R R/html_dependency_jspdf.R R/util_table_of_vct.R R/prep_data_management.R R/util_error.R R/util_finalize_sizing_hints.R R/prep_get_study_data_segment.R R/util_as_character.R R/prep_get_user_name.R R/util_pretty_vector_string.R R/prep_extract_summary.R R/util_empty.R R/prep_load_workbook_like_file.R R/com_item_missingness.R R/util_is_try_error.R R/util_html_for_var.R R/util_parse_date.R R/util_referred_vars.R R/util_user_hint.R R/pipeline_recursive_result.R R/prep_extract_summary.dataquieR_resultset2.R R/util_compress_ggplots_in_res.R R/util_sigmagap.R R/util_rio_import.R R/prep_pmap.R R/util_compare_meta_with_study.R R/print.interval.R R/prep_meta_data_v1_to_item_level_meta_data.R R/int_datatype_matrix.R R/util_setup_dashboard.R R/util_observations_in_subgroups.R R/util_create_page_file.R R/util_app_vc.R R/prep_summary_to_classes.R R/util_as_numeric.R R/summary.dataquieR_resultset2.R R/prep_clean_labels.R R/prep_purge_data_frame_cache.R R/util_histogram.R R/util_3SD.R R/int_unexp_elements.R R/util_app_iav.R R/prep_save_report.R R/reflection.R R/dataquieR_resultset2.R R/util_as_numeric_with_unit.R R/util_is_integer.R R/util_check_data_type.R R/util_app_dc.R R/util_study_var2factor.R R/nres.R R/menu_env.R R/util_standardise_ordinal_codes.R R/plot.dataquieR_summary.R R/util_get_category_for_result.R R/util_ggplot_text.R R/prep_extract_cause_label_df.R R/util_deparse1.R R/prep_create_meta_data_file.R R/zzz_globs.R R/util_melt.R R/util_set_doublequotes.R R/int_unexp_records_dataframe.R R/util_extract_matches.R R/prep_check_meta_data_dataframe.R R/pipeline_vectorized.R R/util_normalize_value_labels.R R/util_add_computed_internals.R R/util_combine_list_report_summaries.R R/dim.dataquieR_resultset2.R R/prep_datatype_from_data.R R/util_find_external_functions_in_stacktrace.R R/prep_acc_distributions_with_ecdf.R R/int_all_datastructure_dataframe.R R/util_attach_attr.R R/util_get_ruleset_formats.R R/prep_render_pie_chart_from_summaryclasses_ggplot2.R R/util_col2rgb.R R/prep_check_meta_data_segment.R R/util_looks_like_missing.R R/html_dependency_vert_dt.R R/prep_add_data_frames.R R/util_all_ind_functions.R R/util_filter_names_by_regexps.R R/html_dependency_dataquieR.R R/util_margins_poi.R R/util_check_one_unique_value.R R/util_remove_na_records.R R/util_is_time_only.R R/html_dependency_report_dt.R R/prep_title_escape.R R/util_gg_get.R R/dq_report2.R R/util_collapse_msgs.R R/int_duplicate_content.R R/util_translate_indicator_metrics.R R/prep_expand_codes.R R/util_normalize_time_only_columns.R R/util_rbind.R R/util_cast_off.R R/prep_valuelabels_from_data.R R/util_startsWith_prefix._or_equals_prefix.R R/util_data_type_conversion.R R/util_warn_unordered.R R/util_handle_complex_data_types.R R/util_dist_selection.R R/util_float_index_menu.R R/util_abbreviate.R R/util_is_valid_missing_codes.R R/util_map_to_other_metrics.R R/prep_get_data_frame.R R/prep_open_in_excel.R R/acc_mahalanobis.R R/int_duplicate_ids.R R/util_coord_flip.R R/util_duplicated_inclding_first.R R/util_no_value_labels.R R/util_get_fg_color.R R/util_find_var_by_meta.R R/int_encoding_errors.R R/acc_cat_distributions.R R/util_app_sm.R R/util_tail_file.R R/util_generate_calls_for_function.R R/acc_distributions.R R/util_generate_table_indicators_descriptors.R R/util_bQuote.R R/util_find_first_externally_called_functions_in_stacktrace.R R/util_varcomp_robust.R R/util_formattable.R R/util_remove_dataquieR_result_class.R R/util_is_numeric_in.R R/int_all_datastructure_segment.R R/util_get_encoding.R R/util_get_combined_code_lists.R R/prep_link_escape.R R/util_get_var_att_names_of_level.R R/util_plot_figure_plotly.R R/util_eval_to_dataquieR_result.R R/util_int_unexp_records_set_segment.R R/util_eval_rule.R R/util_map_all.R R/prep_load_folder_with_metadata.R R/prep_compare_meta_with_study.R R/dimnames_dataquieR_resultset2.R R/util_html_table.R R/util_bar_plot.R R/util_html_attr_quote_escape.R R/print.ReportSummaryTable.R R/util_normalize_cross_item.R R/util_int_breaks_rounded.R R/con_contradictions.R R/util_condition_constructor_factory.R R/util_paste_with_na.R R/int_sts_element_segment.R R/util_app_sl.R R/html_dependency_tippy.R R/util_table_rotator.R R/util_df_escape.R R/util_remove_empty_rows.R R/prep_scalelevel_from_data_and_metadata.R R/util_app_iac.R R/des_summary_continuous.R R/util_align_colnames_case.R R/util_optimize_histogram_bins.R R/util_adjust_geom_text_for_plotly.R R/util_lazy_ggplot.R R/util_queue_cluster.R R/util_find_indicator_function_in_callers.R R/util_heatmap_1th.R R/pro_applicability_matrix.R R/util_generate_anchor_tag.R R/dq_report.R R/util_pairs_matrix.R R/print.dataquieR_result.R R/util_recode.R R/util_validate_report_summary_table.R R/com_qualified_segment_missingness.R R/util_get_concept_info.R R/dataquieR_resultset_verify.R R/int_unexp_records_segment.R R/util_validate_missing_lists.R R/util_round_to_decimal_places.R R/util_has_no_group_vars.R R/000_exception_classes.R R/util_filter_missing_list_table_for_rv.R R/util_margins_bin.R R/util_online_ref.R R/util_all_is_integer.R R/prep_add_cause_label_df.R R/util_extract_indicator_metrics.R R/util_get_rule_sets.R R/util_hide_file_windows.R R/util_get_voc_tab.R R/util_interpret_limits.R R/DOT.template_function_indicator.R R/util_replace_codes_by_na.R R/acc_shape_or_scale.R R/util_gg_var_label.R R/resnames.R R/000_options.R R/acc_end_digits.R R/util_correct_variable_use.R R/int_unexp_records_set.R R/util_app_ol.R R/int_part_vars_structure.R R/util_map_labels.R R/util_split_val_tab.R R/util_create_lean_ggplot.R R/util_parse_redcap_rule.R R/util_generate_calls.R R/util_cll_nm2fkt_nm.R R/util_free_varname.R R/util_app_mar.R R/util_filter_repsum.R R/util_extract_all_ids.R R/util_iframe_it_if_needed.R R/util_hubert.R R/util_render_table_dataquieR_summary.R R/util_ensure_in.R R/prep_fix_meta_id_dups.R R/util_plot2svg_object.R R/util_undisclose.R R/util_app_ed.R R/util_find_free_missing_code.R R/prep_study2meta.R R/prep_dq_data_type_of.R R/util_compress.R R/util_suppress_warnings.R R/prep_extract_classes_by_functions.R R/acc_distributions_ecdf.R R/util_extract_named_groups.R R/util_get_dataquieR_result.R R/util_get_hovertext.R R/util_warning.R R/util_int_duplicate_content_dataframe.R R/util_fix_rstudio_bugs.R R/prep_get_variant.R R/com_qualified_item_missingness.R R/util_ds1_eval_env.R R/droplevels.ReportSummaryTable.R R/con_inadmissible_categorical.R R/util_int_duplicate_content_segment.R R/util_pretty_print.R R/acc_varcomp.R inst/doc/DQ-report-example.Rmd inst/mimetypes/README.md tests/testthat.R tests/testthat/test-con_contradictions_redcap.R tests/testthat/test-dq_report_by_sb.R tests/testthat/test-con_limit_deviations.R tests/testthat/test-util_finalize_sizing_hints.R tests/testthat/test-acc_end_digits.R tests/testthat/test-get_internal_api.R tests/testthat/test-prep_get_data_frame.R tests/testthat/test-util_observations_in_subgroups.R tests/testthat/test-int_sts_element_dataframe.R tests/testthat/test-util_replace_codes_by_na.R tests/testthat/test-prep_render_pie_charts.R tests/testthat/test-acc_loess.R tests/testthat/test-acc_distributions_ecdf.R tests/testthat/test-dataquieR_resultset.R tests/testthat/test-prep_add_missing_codes.R tests/testthat/test-dq_report_by_na.R tests/testthat/test-prep_clean_labels.R tests/testthat/test-util_par_pmap.R tests/testthat/test-util_readr_cols_from_metadata.R tests/testthat/test-util_ensure_character.R tests/testthat/test-util_map_by_largest_prefix.R tests/testthat/test-int_unexp_records_set.R tests/testthat/test-util_warning.R tests/testthat/test-prep_check_meta_names.R tests/testthat/test-function_arguments.R tests/testthat/test-dq_report_by_directories.R tests/testthat/test-util_map_labels.R tests/testthat/test-util_is_valid_missing_codes.R tests/testthat/test-util_queue_cluster.R tests/testthat/test-rbind.R tests/testthat/test-dq_report_by_sm.R tests/testthat/test-util_remove_empty_rows.R tests/testthat/test-int_encoding_errors.R tests/testthat/test-util_ensure_suggested.R tests/testthat/test-util_render_table_dataquieR_summary.R tests/testthat/test-util_dist_selection.R tests/testthat/test-dq_report_by_respvars.R tests/testthat/test-util_startsWith_prefix._or_equals_prefix.R tests/testthat/test-prep_apply_coding.R tests/testthat/test-util_html_attr_quote_escape.R tests/testthat/test-dq_report_by_storr.R tests/testthat/test-util_handle_complex_data_types.R tests/testthat/test-nres.R tests/testthat/test-statichtmlWidget.R tests/testthat/test-acc_univariate_outlier.R tests/testthat/test-util_app_dl.R tests/testthat/test-util_dichotomize.R tests/testthat/test-com_qualified_segment_missingness.R tests/testthat/test-util_correct_variable_use.R tests/testthat/test-acc_distributions.R tests/testthat/test-prep_combine_report_summaries.R tests/testthat/test-dq_report2.R tests/testthat/test-util_no_value_labels.R tests/testthat/test-util_app_loess.R tests/testthat/test-prep_add_to_meta.R tests/testthat/helper-locale.R tests/testthat/test-util_app_sl.R tests/testthat/test-prep_undisclose.R tests/testthat/test-util_set_doublequotes.R tests/testthat/test-acc_margins.R tests/testthat/test-util_parallel_futures.R tests/testthat/test-util_remove_na_records.R tests/testthat/test-util_find_external_functions_in_stacktrace.R tests/testthat/test-util_app_dc.R tests/testthat/test-com_segment_missingness.R tests/testthat/test-acc_varcomp.R tests/testthat/test-util_user_hint.R tests/testthat/test-util_split_val_tab.R tests/testthat/test-prep_load_folder_with_metadata.R tests/testthat/test-util_warn_unordered.R tests/testthat/test-des_summary.R tests/testthat/helper-expect_message2.R tests/testthat/test-com_item_missingness.R tests/testthat/test-util_acc_loess_bin.R tests/testthat/test-util_is_try_error.R tests/testthat/test-dq_report_by_m.R tests/testthat/test-prep_save_report.R tests/testthat/test-util_generate_pages_from_report.R tests/testthat/test-util_interpret_limits.R tests/testthat/test-util_app_vc.R tests/testthat/test-plots.R tests/testthat/test-prep_acc_distributions_with_ecdf.R tests/testthat/test-prep_dq_data_type_of.R tests/testthat/test-util_app_sos.R tests/testthat/test-reflection.R tests/testthat/test-util_validate_known_meta.R tests/testthat/test-util_check_data_type.R tests/testthat/test-util_plot_figure_no_plotly.R tests/testthat/test-prep_study2meta.R tests/testthat/test-resnames.R tests/testthat/test-prep_create_meta_data_file.R tests/testthat/helper-vdiffr-variant.R tests/testthat/test-util_check_one_unique_value.R tests/testthat/test-util_set_singlequotes.R tests/testthat/test-util_check_group_levels.R tests/testthat/test-util_as_numeric.R tests/testthat/test-util_app_iav.R tests/testthat/test-util_find_free_missing_code.R tests/testthat/test-util_detect_cores.R tests/testthat/test-util_app_ol.R tests/testthat/test-util_looks_like_missing.R tests/testthat/test-util_app_mar.R tests/testthat/test-int_unexp_records.R tests/testthat/test-util_app_im.R tests/testthat/test-util_assign_levlabs.R tests/testthat/test-prep_valuelabels_from_data.R tests/testthat/test-util_find_first_externally_called_functions_in_stacktrace.R tests/testthat/test-int_datatype_matrix.R tests/testthat/test-000_globs.R tests/testthat/test-prep_compare_meta_with_study.R tests/testthat/test-prep_pmap.R tests/testthat/test-util_compare_meta_with_study.R tests/testthat/test-util_empty.R tests/testthat/test-util_parse_redcap_rule.R tests/testthat/test-dataquieR_resultset2.R tests/testthat/test-con_contradictions.R tests/testthat/test-meta_data_env.R tests/testthat/test-prep_map_labels.R tests/testthat/test-util_app_hl.R tests/testthat/test-acc_multivariate_outlier.R tests/testthat/test-time_only.R tests/testthat/test-util_app_sm.R tests/testthat/test-prep_create_meta.R tests/testthat/test-dq_report_by_arguments.R tests/testthat/test-util_standardise_ordinal_codes.R tests/testthat/test-prep_get_study_data_segment.R tests/testthat/test-util_unit2baseunit.R tests/testthat/helper-condition_wrapper.R tests/testthat/helper_no_testthat.R tests/testthat/test-acc_shape_or_scale.R tests/testthat/helper-state.R tests/testthat/test-con_inadmissible_categorical.R tests/testthat/test-util_app_mol.R tests/testthat/test-util_ds1_eval_env.R tests/testthat/test-pro_applicability_matrix.R tests/testthat/test-util_plot_figure_plotly.R tests/testthat/test-print-list.R tests/testthat/test-util_disjunct_var_sets.R tests/testthat/test-com_qualified_item_missingness.R tests/testthat/setup.R tests/testthat/test-dq_report_by_pipesymbol_list.R tests/testthat/test-util_get_code_list.R tests/testthat/test-util_contradiction_rules.R tests/testthat/test-print.R tests/testthat/test-dq_report_by_s.R tests/testthat/test-util_set_size.R tests/testthat/test-util_has_no_group_vars.R tests/testthat/test-util_plot_categorical_vars.R tests/testthat/test-prep_title_escape.R tests/testthat/test-util_app_cd.R tests/testthat/test-com_unit_missingness.R tests/testthat/test-util_combine_missing_lists.R tests/testthat/test-util_parse_assignments.R tests/testthat/test-util_map_all.R tests/testthat/test-dq_report_by_gpt.R tests/testthat/test-util_backtickQuote.R tests/testthat/test-prep_min_obs_level.R tests/testthat/test-util_error.R tests/testthat/test-util_app_ed.R tests/testthat/test-acc_varcomp2.R tests/testthat/test-prep_prepare_dataframes.R tests/testthat/test-util_heatmap_1th.R tests/testthat/test-util_app_iac.R tests/testthat/test-prep_datatype_from_data.R tests/testthat/test-int_unexp_elements.R tests/testthat/test-util_varcomp_robust.R tests/testthat/test-acc_mahalanobis.R tests/testthat/test-acc_cat_distributions.R tests/testthat/_snaps/util_varcomp_robust.md tests/testthat/_snaps/util_handle_complex_data_types.md tests/testthat/_snaps/util_parallel_futures.md tests/testthat/_snaps/util_split_val_tab.md tests/testthat/_snaps/int_sts_element_dataframe.md tests/testthat/_snaps/com_segment_missingness.md tests/testthat/_snaps/prep_create_meta_data_file.md tests/testthat/_snaps/util_app_iac.md tests/testthat/_snaps/prep_compare_meta_with_study.md tests/testthat/_snaps/prep_study2meta.md tests/testthat/_snaps/prep_get_study_data_segment.md tests/testthat/_snaps/prep_combine_report_summaries.md tests/testthat/_snaps/prep_add_missing_codes.md tests/testthat/_snaps/int_unexp_records_set.md vignettes/DQ-report-example.Rmd man/print.StudyDataSlot.Rd man/SEGMENT_ID_TABLE.Rd man/DATA_PREPARATION.Rd man/dataquieR.VALUE_LABELS_htmlescaped.Rd man/dq_report_by.Rd man/util_filter_repsum.Rd man/ASSOCIATION_DIRECTION.Rd man/DISTRIBUTIONS.Rd man/prep_get_data_frame.Rd man/dataquieR.lang.Rd man/dataquieR.ERRORS_WITH_CALLER.Rd man/dataquieR.lazy_plots.Rd man/VARATT_REQUIRE_LEVELS.Rd man/pow-.numeric_with_unit.Rd man/dot-get_internal_api.Rd man/COMPUTATION_RULE.Rd man/int_sts_element_dataframe.Rd man/summary.dataquieR_resultset2.Rd man/prep_clean_labels.Rd man/meta_data_segment.Rd man/dataquieR.grading_rulesets.Rd man/progress_init_fkt.Rd man/dataquieR.MAX_LONG_LABEL_LEN.Rd man/prep_render_pie_chart_from_summaryclasses_plotly.Rd man/prep_create_storr_factory.Rd man/util_int_duplicate_ids_dataframe.Rd man/DF_NAME.Rd man/meta_data_env.Rd man/prep_map_labels.Rd man/MISS_RESP.Rd man/html_dependency_jspdf.Rd man/SEGMENT_RECORD_COUNT.Rd man/prep_extract_cause_label_df.Rd man/acc_multivariate_outlier.Rd man/MAHALANOBIS_THRESHOLD.Rd man/dataquieR.CONDITIONS_WITH_STACKTRACE.Rd man/droplevels.ReportSummaryTable.Rd man/prep_acc_distributions_with_ecdf.Rd man/prep_extract_summary.dataquieR_resultset2.Rd man/pro_applicability_matrix.Rd man/rbind.ReportSummaryTable.Rd man/CHECK_LABEL.Rd man/slash-.numeric_with_unit.Rd man/print.ReportSummaryTable.Rd man/dataquieR.acc_loess.plot_observations.Rd man/dataquieR.old_factor_handling.Rd man/con_contradictions.Rd 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